Exploring the structure and function of microbial communities

“Everything is everywhere…” gets us nowhere

By: Noah Fierer

Microbial ecology has surprisingly few unifying concepts. It is difficult to identify ‘rules’ or paradigms that apply across the field of microbial ecology regardless of the taxonomic group or environment in question. Here is my short list and I realize I am probably missing quite a few obvious ones:

Bacterial cell size is inversely correlated with generation time – slow growers tend to be smaller in size.

If a metabolic strategy is thermodynamically feasible, there is some microbe somewhere that uses that strategy.

In most environments, the majority of taxa are rare.

Microbes, like ‘macrobes’ follow the species-area relationship –the larger the area surveyed, the more taxa found in that area.

Most microbes are difficult to culture in vitro (not impossible – just difficult)

“Everything is everywhere, but the environment selects”

These are just a few that came off the top of my head – and I realize that these ‘unifying concepts’ are pretty bland and not particularly specific. We’re ecologists not physicists.

I want to focus here on the last one “Everything is everywhere, the environment selects”. This statement comes from Lourens Baas-Becking in 1934 and it summarizes ideas promoted by his predecessor, Martinus Beijerinck (see O’Malley 2008 for an excellent review of the history behind this statement). It has since become one of the most commonly mentioned phrases in microbial ecology talks and papers. “Everything is everywhere…” is our mantra and our siren song.

In its essence “Everything is everywhere…” is another way of saying that for microbes there are no dispersal constraints and thus it is the environmental conditions that determine what taxa are where, not dispersal capabilities. Or as stated by Fenchel and Finlay (2004) : “habitat properties alone are needed to explain the presence of a given microbe, and historical factors are irrelevant”.

To some degree this could be considered a simplified corollary of the ‘niche versus neutral theory’ debate – a debate that has spawned hundreds of papers over the decades in the broader field of ecology.

There is nothing wrong with ‘everything is everywhere….’ it is clearly useful as a null hypothesis. However, as a concept to drive research programs – it is nearly useless. Why? – because we already know it is wrong. Everything cannot be everywhere.

Depending on the temporal or taxonomic resolution being investigated it may appear that microbial dispersal is unlimited. Members of the Bacteroidetes phylum can be cultured from every human gut, every soil has Actinobacteria – but this does not mean all variants of a given bacterial ‘species’ are everywhere. If I open the lid of a petri plate and expose it to the atmosphere for 1 hour, as many as 104 bacterial cells could land on it. Even if every one of these cells represented a distinct species, this would be a far cry from the total estimated number of bacterial ‘species’ that likely exist on the planet (an unknown number but given that a single environment type – soil in Central Park, NYC – harbors >105 different bacteria and archaea– the final number of species found across every environment on Earth is undoubtedly a huge number). All this silly example demonstrates is that it is mathematically impossible for everything to be everywhere – there are undoubtedly dispersal constraints that influence community assembly, particularly across shorter time scales or when examining communities at finer levels of taxonomic or phylogenetic resolution.

Of course, we already know from the long history of research on animal and plant pathogens that microbes are not instantaneously dispersed across the planet. There are clearly constraints on the dispersal of microbial pathogens and their dispersal patterns can often be quantified in real time.

What is the utility of treating ‘everything is everywhere’ as a valid hypothesis if we already know it is not true?

The paradigm of ‘everything is everywhere, the environment selects’ is clearly an oversimplification. If we want to move the field forward, we should get rid of presenting hypotheses that we already know to be invalid. Although not as catchy, a better slogan might be “When, where, and why is dispersal important in structuring microbial communities?”.

4 thoughts on ““Everything is everywhere…” gets us nowhere”

Duuuuude. Everything is everywhere is way easier. Let’s just keep it simple so we can up the retweets. The public is done learning. It is the age of telling, and the stories need to be real simple, like Sarah Palin. It’ll work out splendid, no worries here. Love, Nero.

I like the list.
I agree, if you’re talking about individual microbial taxa, then no, of course everything is not everywhere. But, what is more interesting to me is potential function, where microbial community ecology meets ecosystem ecosystem ecology. Is the potential for every microbial function everywhere? Especially basic, carbon-mineralizing functions of free-living microbes. It has been demonstrated that inocula from different soils exhibit different functions sealed jars, but I don’t think it has been demonstrated in an actual ecosystem, where soils are constantly bombarded with wind-, dust- and water-borne inocula. Is microbial function ever dispersal limited? Are there any cases in which we can inoculate real soils and alter function, say decomposition rates, in situ? This is the key test for me.

I like the list too. Perhaps ‘everything is everywhere’ is not meant to be absolute but relative to other organisms; compared to eukaryotes with more limited dispersal abilities then microbia are everywhere. Terms like cosmopolitan and endemic are useful in biogeography but also context dependent.

I happen to work on macrofungi, and the dominant pattern is regional endemism. Why? Unlike bacteria, macrofungi are rather finicky about their sex partners. Imagine landing on an island surrounded by ocean and trying to find an opposite mating type within a few centimeters of where you landed! Then if you need a particular host plant to survive, what is the probability of landing near a suitable host AND a spore or mycelium of an opposite mating type of the same species? I also work in the Neotropics (Caribbean), and the pattern shown for soil fungi follows Rappaport’s rule, as it does for plants and animals. Tropical fungi (and plants & animals) are apparently more sensitive to environmental fluctuations or changes, so they have smaller geographic distributions than species of the same groups that live at higher latitudes (See Tedersoo et al. 2014, Science).